RNA Detection

each lane between 30 and 150 bp from the first dimension gel (Fig.3a). The second dimension gel can usually accommodate three ge ...

until all of the filtered RNA sample flowed through the column. Wash the column with 300μL water and spin the column at 4 C, 1 ...

Add 8μL reverse transcriptase mix to the RNA and heat the samples at 25C for 3 min, 42C for 5 min, 52C for 30 min; hold at 4 ...

Remove the supernatant and wash the beads twice with 80% ethanol at RT. Elute DNA with 10μL water twice each tube (~20μL eluate ...

file name prefix is x. The following are a preferred set of file name conventions. Having standard file names makes the man- age ...

end adapter sequences x_trim_nodup_bcnn_starSSAligned.out. sam: reads mapped to STAR index for species SS, normally aligned. x_t ...

Convert SAM to BAM format, sort the BAM file and extract primary mapped reads using SAMtools [24]. samtools view -b -F 0x900 - ...

perl samPairingCalling.pl -i x_Aligned_prim_N.sam -j x_Chimeric.out.junction -s x_Chimeric.out.sam -o x_geometric -g genome.fa - ...

example represents a hypothetical stem loop (also described here:https://www.broadinstitute.org/igv/node/284). track graphType¼a ...

from miRBase, and/or nonredundant RNAs from the human transcriptome annotations as references. After mapping reads to these refe ...

Phylogenetic analysis of RNA structure. The two arm intervals of each DG were used to extract multiple alignments from whole-ge ...

4 Notes The 30 min irradiation time was chosen for strong cross- linking; however, shorter times may be useful for certain appl ...

rRNAs, mitochondrial rRNAs, snRNAs, and XIST. A STAR index is needed for each reference. To make these mini- reference STAR indi ...

Acknowledgment The authors wish to thank Dr. Howard Chang at Stanford Univer- sity for his generous support and encouragement. Z ...

Calvet JP, Pederson T (1981) Base-pairing interactions between small nuclear RNAs and nuclear RNA precursors as revealed by pso ...

Chapter 5 Axon-TRAP-RiboTag: Affinity Purification of Translated mRNAs from Neuronal Axons in Mouse In Vivo Toshiaki Shigeoka, J ...

information on the untranslated regions (UTRs) of isoforms, which would be lost by RNase treatment, although the ribosome profil ...

ribosome–mRNA complexes from the superior colliculus (SCs) in the midbrain, where RGC axons terminate, and enables transla- tion ...

Liquid nitrogen in a container (seeNote 2). Dissection tools: forceps, fine scissors, and springbow dissect- ing scissors. 2.2 ...

3.2 Tissue Preparation In order to minimize the RNA degradation, prepare the snap- frozen tissue samples as quickly as possible. ...